Backlash/Feedback on NASA’s Arsenic Findings

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I’m not a biologist – just a journalist who specializes in space and astronomy — so I won’t pretend to be knowledgeable about NASA’s announcement last week of the weird life in a California lake that appears to be able to live with arsenic instead of phosphorous. But I did want to bring to our reader’s attention some various points of view on the topic that have emerged since last Thursday’s press conference.Microbiologist Rosie Redfield at the University of British Columbia has written what could be called a “take-down” of the science paper by Felisa Wolfe-Simon and her team. It is a detailed and thorough review, and her bottom line is: “Lots of flim-flam, but very little reliable information.”

Her opinion was quickly seconded by many other biologists/bloggers, as you can read in David Dodds post at Wired, and also this post by Larry Moran, a Professor in the Department of Biochemistry at the University of Toronto.

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16 Replies to “Backlash/Feedback on NASA’s Arsenic Findings”

Such doubts are always terrible in science when your own scepticism is validated. The questions I posted might turned out to be awfully close to the truth. As I said to bloggers Cappar and Run

Are you cynical of this story, and have questioned it implications?
Do you think this important or panspermia driven (possibly with alliterative motives)?
Did NASA’s press release on all the television news programs with Felisa Wolfe-Simon really creeped you out? (Her [almost] demonic look was much of a concern [to me])
Why did she desperately avoid looking directly at the camera?
Is she being deceptive?
Does Felisa Wolfe-Simon groundbreaking oceanographic research on using arsenic for photosynthesis really just seems a little too convenient?This is why critical thinking is so important.

Her avoiding the cameras and body language at the press release, speaks volumes of her uncertain demeanour to the conclusions made here.

IMO, I think the kind of story just feeds the non-scientifically trained sceptics, and just adds more confusion that science and scientific announcements are untrustworthy or are ‘faith-based.’

If this scientific discovery turns out to be true, then discrediting this individuals is not enough, and a strong message should be sent that it is unacceptable. I.e. They are force to entirely repay the costs of their tertiary education cost for fraudulent behaviour. Extreme. Yes Yet it does send a clear message of the consequences of misleading or unsupportable research.
The continued misleading damage this does in the minds of the general public is immeasurable — to the extent they don’t trust science, the technology it produces, and how the world works. It makes all the complex work done in universities, laboratories and science institutions all that so much harder.

In the end, if when true alien life is found, it is somewhat tarnished by those clambering for the spotlight just to make their research more appealing for the sake of ego. Pity

You remind me of “Kreml whisperers” of earlier, that tried to read their own story in anecdotal events and individual behavior. You can’t and more importantly you shouldn’t try to read what you believe into haphazard events.

As for the science, the process isn’t broken and it remains sound – this is how it should be. What could be improved is NASAs (and Davies) unfortunate tendency to inflate small results. Especially when they obviously is of the type “when you just want to show that your hypothesis is true” as Redfield so clearly described it, are then really suspect and need to be tested later.

What is broken is the embargo process. Several analysts noted as Qev here that NASA could (and have earlier) corrected what would not be presented.

I didn’t think it was a big deal. When I got wind of the coming press release, I figured the statement would be about unusual biology or something that could live in harsh conditions. I’m not sure if this is NASA’s fault for hyping it up, or everyone else fault for assuming it was going to be “THE” announcement. Maybe both. I didn’t think it was a big deal, and I figured the statement would be about unusual biology or something that could live in harsh conditions.

I did get a bit irritated with NASA for letting everyone run with the “omg alien life!!!11!” thing before the embargo was lifted. Was it too much to ask for one person in some position of authority to say, “Settle down, no, it’s not aliens”?

The results are ambiguous, which is why one need to piece together nucleotides with arseno-diester bonds and see if the RNA or DNA function, or if it can be replicated. One needs to do some basic molecular biology, but with arsenated nucleotides.

I appreciated Dr. Alex Bradley’s take on it from a chemist’s vantage point. It came across in a professional and scientific manner. I wasn’t too impressed with Redfield’s political posturing. Here is what Dr. Bradley wrote:

At last during end of this year, human hv made another totally new discovery. As a researcher in the close area, i see Nobel price candidate/s if s/he able to decode the life system of the bacteria & making use of it in research works; just as the thermal-stable bacteria that live in hot spring & end up with daily usage in DNA laboratory worldwide. Really a new knowledge =)

Ironically, Rosie Redfield’s response repeats the sins of the offender she is bashing (which might be true) – she seems highly motivated by an agenda herself, and she’s mostly poking holes at the methodology and psychology of the authors, not at the results themselves. (e.g. – what do the meteor claims, by other scientists, have to do with this ?!)

Of course, being a critique, she doesn’t have to hold the same standards.

Given that the critique of the methodology seems to have valid points, the authors should respond.

Luckily, this seems an easy enough issue to resolve – the samples are here, and we’ll definitely get more eyeballs on the issue now.

In the Netherlands several biologists en chemists have critisized the Science article of Felisa Wolfe-Simon’s team. I wrote a blog about in (OK in Dutch, just try it. 🙂 It’s here: http://www.astroblogs.nl/2010/12/04/nederlandse-biologen-twijfelen-aan-arseenbacterie/). Main objection to the theory of GFAJ-1, which according tot Wolfe’s team has build a DNA-structure from arsenic, is that there’s still some phosphor inside GFAJ-1. And despite the minimal abundance of the phosphor, they (the dutch biologists) think that’s enough for GJAF-1 to build it’s DNA upon. So the bacterium GFAJ-1 hasn’t got an arsenic based DNA-structure, it’s still phosphorous.

The recent announcement by NASA scientists and their collaborators that the GFAJ-1 strain of the Halomonadaceae bacteria provides hints into the potential biology of alien life-forms and the response of the media and scientific community to this claim have revealed several disturbing trends. These include the desperation of a government-funded science agency to generate publicity at a time when its financial support is in jeopardy; the inadequacy of the experiments by these researchers to support their conclusions; the relatively poor peer-review by one of the most prestigious of scientific journals; and the extra-hype added by the mass media. One rather positive aspect of this affair is the rapid response of the scientific community to question and challenge the most poorly supported and far reaching claims. It is likely that they will be disregarded much faster than the previous announcement by NASA of petrified Martian life in an Antarctic meteorite.

A few of my colleagues as well as numerous bloggers have noted that the NASA publicity machine has been coincidently cranked up at a time when the next US budget, including the funding for NASA, is under question. The discovery of the model organism described in the Wolfe-Simon et al. paper in Science is actually not new. Since the mid-nineties, the ongoing study of various strains of Halomonadaceae bacteria and their respiration of arsenic at Mono Lake, the Aberjona Watershed and elsewhere has been reported by Dr. Ronald Oremland (the senior author of the Wolfe-Simon et al. paper) and independently by others.

The central claim of the new Wolfe-Simon et al. study is that arsenic can substitute for phosphorus to sustain the growth of the GFAJ-1 bacterial strain, and some evidence is offered that the arsenic is incorporated into macromolecules such as nucleic acids and proteins. The GFAJ-1 cells were cultivated in the near absence of phosphorus in the growth media in the presence of arsenic. However, the media used in the study apparently had about 3 µM phosphorus, and one wonders whether phosphorus may have also been introduced with the culture plates that may have been pre-washed with phosphate-containing detergents. In any event, the cultured GFAJ-1 cells were still observed to contain phosphorus at about 1% of the levels seen in cells grown in the presence of high phosphorus. Even under these conditions, bathing in medium containing arsenic, these cells still featured 100-times more phosphorus than arsenic. Moreover, the levels of arsenic incorporated into the phosphorus-depleted bacteria was not that much different from phosphorus-supplemented GFAJ-1 cells grown without arsenic. Ideally, a synchrotron X-ray analysis of arsenic in biomolecules should have been undertaken for both the phosphorus-fed and starved populations of the bacteria rather than just the phosphorus-depleted cells as was performed in the study.

Despite the speculations offered in the Wolfe-Simon et al. paper, no conclusive evidence was provided that any arsenic actually replaced phosphorus in the DNA backbone of the GFAJ-1 cells. To incorporate arsenic into nucleotides and proteins, the arsenic would have to be presented with the arsenic-containing equivalent of adenosine tri-phosphate (ATP), i.e. adenosine tri-arsenate (ATAs). No evidence was obtained for the presence of ATAs in the GFAJ-1 bacteria. In fact, I have been unable to find any reports of ATAs in any life-form from PubMed or Google searches.

While arsenic and phosphorus are highly related in the periodic table of elements, the arsenic atom is slightly more than double the molecular mass of phosphorus. As atoms get larger, the electronic structure of the atom, particularly those parts that participate in chemical bonds, become increasingly diffuse. Consequently, arsenate esters are very unstable and hydrolyze markedly faster than phosphate esters. This instability of arsenate ester linkages really restricts their utility in the synthesis of macromolecules like DNA. Furthermore, the instability of arsenylation of proteins, would precludes it from effectively replacing protein phosphorylation. Protein phosphorylation appears to be the major post-translational regulatory mechanism for the emergence of eukaryotic organisms and seems to be required for the development of multi-cellular organisms.

While the existence of stable ATAs is doubtful, it is more feasible that adenosine-diphosphate, mono-arsenate (ADPAs) might be produced that could fuel arsenylation reactions. Even if ADPAs exists, it is still difficult to reconcile the use of arsenate by a wide range of enzymes to replace all of the diverse metabolic and structural roles (e.g. nucleic acids, phospholipids, phosphoproteins) of phosphate in even bacteria. It is unlikely ADPAs would have a stable enough high energy bond between the gamma arsenic and oxygen atoms to serve as an efficient source of chemical energy. ATP is optimal in all biological systems on this planet with an intermediary position between the higher energy compounds from which ATP accepts phosphate and the lower-energy compounds from which it donates phosphate. Consequently, an organism that exclusively utilizes arsenic and not phosphorus would have a profoundly different metabolism with very different metabolites and macromolecules.

As a member of the wide-spread Gammaproteobacteria, the Halomondadaceae bacteria clearly do not represent an alternatively evolved family of life-forms, but are well adapted to endure extreme conditions. These organisms are also commonly dispersed in environments in which “normal” microbes proliferate, which is most probably where they originated. The GFAJ-1 bacteria actually prospered better in the presence of phosphorus. Those grown in the presence of arsenic and near absence of phosphorus became bloated in size by approximately 60%. This was due to the appearance of large “empty” vacuoles in the bacteria. It seems that this organism functions optimally in phosphorus, but tolerates arsenic. This is not surprising, since the concentration of phosphorus in the Earth’s crust is around 1000 parts per million (ppm), which is about 500-times higher than measured for arsenic. Such a relative distribution of these two elements is likely to be universal, as more energy is required to forge arsenic atoms than phosphorus atoms.

Many metals can poorly mimic each other as cofactors in enzyme-catalyzed reactions. This is why a few are highly toxic such as lead and mercury. The fidelity of enzymes for their optimal elements is not 100%, so it is not surprising if trace arsenic can replace phosphorus in the structures of small molecules and macromolecules. Many marine organisms, including clams and sea weeds can also accumulate arsenic. This is likely to be a protective response to reduce the threat of predation by animals that might try to consume them. Arsenic is particularly toxic in eukaryotic organisms, because amongst other many other problems, arsenic inhibits pyruvate dehydrogenase in the citric acid cycle and it uncouples oxidative phosphorylation in the mitochondria, both of which inhibit ATP synthesis. It seems probable that the Halomonadaceae bacteria have acquired the ability to tolerate arsenic, most likely to avoid being eaten. They may concentrate arsenic-containing compounds in vacuoles for this purpose, and they are known to excrete arsenic, presumably when it becomes too toxic for the bacteria themselves. This ability provides the opportunity for these bacteria to thrive in arsenic-rich environments where most other bacteria cannot.

The lessons from all of this hype from a US government agency, a peer-reviewed scientific journal, and the popular press will likely go unheeded. Unfortunately, too many research institutions that depend on public funding through government agencies and charity will continue to feel pressured to over blow their latest scientific breakthroughs to justify the massive amounts of financial support that they have received. However, with the increasing ability of the wider scientific community to rapidly challenge these assertions in the Internet age, they do so at the peril of their credibility.

Thank you so much for your articulate rebuttal that this layman understood. I do hope NASA and the media “responsible” for science reporting is reading these UT responses to this and other questionable “breakthrough” articles.

I should comment that your last paragraph is highly significant, and shows the difficulties (and pressures) in producing results and balance this in answering towards their funding masters; governments, corporations, etc.

I think this is a growing problem — especially as the experiments gets more complicated; and become more out of reach in understanding the story to the average Joe. Justification for experimental science in the internet age, means all the other competing projects has an enhanced and increased rivalry.